Explore a River Health Assessment of the lower Tuolumne River watershed presented as an interactive map. You can select/unselect relevant layers for five watershed sections. The river health assessment was developed by a collaboration of the Water & Climate Justice Lab, two capstone teams at Santa Clara University, and the Yosemite River Alliance (Modesto Office). The map includes analysis on the distribution and proximity of irrigated farmland, protected areas, riparian habitat, sources of pollution, and community infrastructure in five sections of the lower watershed, below San Pedro Dam.

Overview

The health of a river is inseparable from the well-being of the people and ecosystems that depend on it. Yet, rivers across the United States are under increasing pressure from human activity. Even with protections under the Clean Water Act,  many rivers continue to face pollution, reduced connectivity, and declining ecological function. These pressures affect the human and non-human (i.e. fish) communities in and along these rivers. The Tuolumne River, which runs through the Central Valley and Modesto regions, exemplifies this tension. In addition to its historical significance during the Gold Rush, the river continues to supply water for agriculture, sustain local ecosystems, and meet the daily needs of surrounding communities. Farmers rely on the water to irrigate crops that feed the region and beyond. Local residents depend on the river for drinking water, recreation, and connection to the natural environment. The river also supports habitats for fish, birds, and other wildlife, contributing to regional biodiversity. Wildlife and biodiversity directly influences the communities that rely on rivers for drinking water, farming, recreation, and cultural practices. These overlapping dependencies mean that changes in water quality, flow, or ecological health have cascading effects for both people and nature.

Understanding how land use, industrial activity, and climate change affect the Tuolumne, therefore, is essential. By examining the relationships between human activity and watershed health, this study provides insight into how local decisions shape water quality, ecosystem function, and community well-being. The goal is to identify patterns that can inform more sustainable land management practices and strengthen the resilience of the Modesto region and the Central Valley as a whole. Protecting the Tuolumne is not only about preserving a river; it is about safeguarding the communities, agriculture, and ecosystems that rely on it today and into the future.

The WCJL partnered with The Yosemite Rivers Alliance to conduct this work. The Yosemite Rivers Alliance works to protect and restore rivers in the Sierra Nevada and Central Valley through pollution reduction, habitat improvements, and supporting the long-term resilience of the rivers, making sure they stay healthy for both people and ecosystems. This project aligns with their mission by looking at the health of the Tuolumne River and how human activity and land use affect water quality and habitats. By analyzing these patterns, we can provide information that helps guide better land and water management. Working with the Yosemite Rivers Alliance ensured that findings supported local efforts to protect the river. 

What we found is that composite river health scores varied across the five sections of the Tuolumne River, reflecting differences in water quality, land management, ecosystem condition, and water flow. Section 1 had the highest composite score (3.610), while Section 3 had the lowest (2.158), showing that river health is unevenly distributed along the watershed. Water Quality was the primary driver of variation, largely influenced by nitrates and surrounding land use. Sections with high percentages of irrigated farmland, such as Section 3, scored lower on Water Quality metrics, while Sections with less intensive agriculture or low industrial activity, like Section 1, maintained higher scores overall despite some nitrate concerns.

How the River Health Assessment Works

The River Health Assessment  focused on four main categories: water quality, water flow, land management, and ecosystem status. Each category included several sub-categories to capture different aspects of river health, allowing for a comprehensive evaluation. We used a weighted grading system to account for the differences in impact of the categories and sub-categories.  Water quality was weighted the highest at 40%, and the remaining three categories were weighted equally at 20% each. Within each category, subcategories were weighted with more important factors receiving higher weightings. For example, the score for water quality was calculated by assigning each measure a subscore, multiplying it by its indicator weight, summing these weighted subscores, and then applying the 40% weight toward the overall river health grade. Explore each of the four categories in more detail below.

I. The Four Main Categories

Water Quality 

Water quality was weighted the greatest at 40% of the total grade, reflecting its critical importance to human and ecosystem health. Subcategories included water quality testing measures (including nitrates from agricultural runoff), conductivity, dissolved oxygen, and pH, as all of these factors directly influence river health. These measures were combined with land-use indicators: agricultural land cover (33% of the water quality subscore), presence of industrial infrastructure such as food processing plants and wineries, and auto repair shops (33%), and the presence of mobile home parks (16.5%).

Water Flow

Water flow was weighted at 20% of the total grade, making it equally weighed with Land Management and Ecosystem Status. Water flow is an extremely important variable for river health, as it controls factors like oxygen levels, habitat conditions, and sediment flow. To assess water flow in the Toulmene, river flow data was examined to capture changes in hydrologic conditions. Specifically, the percentage of flow in each section of the river compared to the La Grange section were converted into letter grades.

Land Management

Land Management was weighted at 20% of the total grade. Land management considered the percentage of protected areas within one kilometer of the river. Protected areas were identified through a shapefile of protected lands from the San Joaquin County government.

Ecosystem Status

Ecosystem status was weighted at 20% of the total grade. Surrounding ecosystems directly influence river health, so it is important to consider ecosystem health when assessing overall river health. Ecosystem status was assessed through indicators of riparian coverage (67% of the ecosystem status subscore), riparian quality (67%), and invasive species counts within one kilometer of the river (67%). Riparian coverage refers to the plant life, trees, and ground cover growing along the banks of the river, and the riparian quality refers to the health of said plants.

II. Details on the Grading Scheme

Water Quality

The four main categories evaluated for Water Quality were Dissolved Oxygen (mg/L), Conductivity (µS/cm), Nitrate Concentration (mg/L), and river pH. Each category was broken into ranges that correspond to a letter grade (see Table 1). 

Grade	DO (mg/L)	Conductivity (µS/cm)	Nitrate (mg/L)	pH
A	9.5 - 12	0 - 200	0 - 1.0	6.4 - 7.2
B	6.5 - 9.4	201 - 500	1.1 - 3.0	(6.0 - 6.3), (7.3 - 8. 4)
C	4.0 - 6.4	501 - 1000	3.1 - 5.0	(4.5 - 5.9), (8.5 - 10)
D	1 - 3.9	1001 - 10,000	5.1 - 10.0	(3.0 - 4.4), (10.1 - 11.5)
F	0 - 0.9	10,000+	10.0+	(0 - 2.9), (11.6 - 14)

Table 1: Grading Scale for Water Quality Testing. Rubric to convert the different measures of water quality in each watershed section into letter grades. 

For the purposes of this project, we examined how surrounding land use influences the health of the Tuolumne River and its watershed. Land use provides a way to see how different human activities place pressure on river systems. Agricultural land can contribute nutrient runoff, industrial sites may introduce pollutants, and patterns of housing development can shape exposure to environmental risk.  Land-use indicators were broken into four categories: agricultural land cover, presence of industrial infrastructure (food processing plants, wineries, auto repair shops), and presence of mobile home parks. Examining these patterns helps reveal how decisions on the landscape influence water quality and ecosystem conditions along the river. Below are the rubrics for the data generated by this study (Table 2 - 5). 

 

Grade	Percent Coverage of Important Irrigated Farmland
A	0.0 – 8.3
A−	8.3– 16.7
B+	16.7 – 25.0
B	25.0– 33.3
B−	33.3– 41.7
C+	41.7 – 50.0
C	50.0 – 58.3
C−	58.3 – 66.7
D+	66.7– 75.0
D	75.0– 82.5
D-	82.5– 90.0
F	> 90.0

Table 2: Agricultural land cover rubric. Rubric to convert the percent of important irrigated farmland in each watershed section into letter grades.

Grade	Density of Auto Repair Shops per Square Kilometer
A	0.0 – 0.08
A−	0.08 – 0.17
B+	0.17 – 0.25
B	0.25 – 0.33
B−	0.33 – 0.42
C+	0.42– 0.50
C	0.50 – 0.58
C−	0.58 – 0.67
D+	0.67 – 0.75
D	0.75 – 0.83
D-	0.83 – 0.92
F	> 1.000

Table 3: Auto repair shop rubric. Grading scale used to convert auto repair shop density (shops per km²) into letter grades for the industrial presence metric.

Grade	Percent Coverage of Wineries and Food Processing Plants
A	0.00 – 0.33
A−	0.33 – 0.67
B+	0.67 – 1.00
B	1.00 – 1.67
B−	1.67 – 2.33
C+	2.33 – 3.00
C	3.00 – 3.67
C−	3.67 – 4.33
D+	4.33 – 5.00
D	5.00 – 7.50
D-	7.50 – 10.00
F	> 10.00

Table 4: Wineries and food processing plants rubric. Grading scale used to convert percent coverage of wineries and food processing plants into letter grades for the industrial presence metric.

Grade	Density of Mobile Home Parks per Square Kilometer
A	0.0 – 0.08
A−	0.08 – 0.17
B+	0.17 – 0.25
B	0.25 – 0.33
B−	0.33 – 0.42
C+	0.42 – 0.50
C	0.50 – 0.58
C−	0.58 – 0.67
D+	0.67 – 0.75
D	0.75 – 0.83
D-	0.83 – 0.92
F	> 1.00

Table 5: Mobile home presence rubric. Grading scale used to convert mobile home park density (home parks per km²) into letter grades for the mobile home parks presence metric.

Water Flow 

To further evaluate the health of the river, water flow rates were considered. We used the percent of flow compared to the La Grange region to quantify water flow rates throughout the Toulmene river basin. A detailed grading scheme is included below (Table 6). 

Grade	% of Flow Compared to La Grange
A	100-80
B	79-60
C	59-40
D	39-20
F	<19

Table 6: Grading scale for percent flow compared to La Grange. Rubric to convert the percent of river flow in each watershed section compared to river flow in La Grange into letter grades.

Land Management 

To evaluate land management, we added a one km buffer around the river and calculated the % of protected land within the buffer zone. Protected land is an important indicator of overall river health because nothing can be built on this land, and thus there are no pollutant sources. Areas where 25% of the area in the buffer zone was protected land ranked the highest receiving an A, and areas where 5% or less of the area in the buffer zone was protected received a grade of F. See the detailed grading scheme for land management below (Table 7).

Grade	Protected Areas (% protected area within 1 km of river)
A	>25
B	15-24.99
C	10-14.99
D	5-9.99
F	<5

Table 7. Grading Scale for Percent Protected Areas. Rubric to convert the percent of protected areas within 1 kilometer of the river in each watershed section into letter grades

Ecosystem Status

To evaluate the ecosystem status of the river, three metrics were considered: the percent of invasive species present, riparian coverage (% within 1 km buffer of river) and riparian quality (% of low/no invasive species). Areas that had a lower prevalence of invasive species received better grades. Areas where riparian coverage and riparian quality were higher also received higher grades. See the detailed grading scheme below (Table 8). 

 

Grade	Percent Invasive Species Prevalence	Riparian coverage (% within 1 km of river)	Riparian quality  (% low/no invasive species)
A	0-19	>25	80 - 100
B	20-39	15-24.99	60 - 80
C	40-59	10-14.99	40 - 60
D	60-79	5-9.99	20 - 40
F	80-100	<5	0 - 20

Table 8. Grading Scale for Ecosystem Status. Rubric to convert the percent of invasive species prevalence, percent of riparian coverage within 1 kilometer of the river, and percent of low/no invasive species in each watershed section into letter grades

Overall Grading Scheme

To assign a composite grade to each river section, individual environmental metrics are evaluated on a standard GPA scale (0.0 to 4.0) and weighted by their relative importance within subcategories to generate metric totals. These totals form four core topic scores—Water Quality (40%), Water Flow (20%), Land Management (20%), and Ecosystem Status (20%)—which are then weighted and combined into a final Composite Score out of 4.0. For example, the Dos Rios to Modesto section (see Table 9) earned a Composite Score of 2.83 (a C+ equivalent), where strong results in general water parameters (pH, dissolved oxygen) and minimal industrial impact were offset by high agricultural land cover, elevated nitrates, invasive species, and moderate river flow metrics.

Topic (Weight)	Metric (Weight)	Measure	Grade	Score	Metric Avg.	Weighted Metric Score	Metric Total	Topic Score	Composite Score
I: Water Quality (0.4)	Water Quality Testing (0.165)	Nitrates (ag. runoff)	D+	1.3	3.325	0.548	2.710	1.084	2.828
		Conductivity	A	4
		Dissolved O2	A	4
		pH	A	4
	Agricultural Land Cover (0.33)	Percent of watershed area that is irrigated land	D-	0.7	0.7	0.231
	Industrial Presence (0.33)	Percent area by food processing plants or wineries	A	4	4	1.32
		Density of auto repair shops per Square Kilometer	A	4
	Mobile Home Park Presence (0.165)	Density of Mobile Home Parks per Square Kilometer	A-	3.7	3.7	0.610
II: Water Flow (0.2)	River Flow Data	% flow	C	2	2	NA	NA	0.4
III: Land Management (0.2)	Protected Areas	% protected area within 1 km of river	B-	2.7	2.7	NA	NA	0.54
IV: Ecosystem Status (0.2)	Riparian Coverage (0.67)	% Riparian within 1km of river	C+	2.3	2.3	1.541	4.02	0.804
	Riparian Quality (0.67)	Riparian within 1km of river	B-	2.7	2.7	1.809
	Invasive Species (0.67)	Invasive Species Count	D	1	1	0.67

Table 9. Weighted grading framework for the Dos Rios to Modesto section showing categories, subcategories, and indicator weights used to calculate overall Tuolumne River health.

III. Detailed Findings 

Composite river health scores varied across the five sections of the Tuolumne River, reflecting differences in water quality, land management, ecosystem condition, and water flow. Section 1 had the highest composite score (3.610), while Section 3 had the lowest (2.158), showing that river health is unevenly distributed along the watershed. Water Quality was the primary driver of variation, largely influenced by nitrates and surrounding land use. Sections with high percentages of irrigated farmland, such as Section 3, scored lower on Water Quality metrics, while Sections with less intensive agriculture or low industrial activity, like Section 1, maintained higher scores overall despite some nitrate concerns.

Ecosystem Status also shaped the composite grades, particularly through riparian coverage, riparian quality, and invasive species prevalence. Section 3’s riparian zones were degraded and fragmented, which further reduced its overall score. In contrast, Sections 1 and 5 had healthier and more continuous riparian habitats, which supported stronger Ecosystem Status grades. Land Management, measured as the proportion of protected areas within 1 km of the river, contributed less to the overall score due to its lower weighting but still provided small boosts in Sections 1 and 5. Water Flow grades were relatively high across the watershed, with minor reductions in Sections 4 and 5 corresponding to urban and agricultural demands.

Looking more closely at land use, the percentages of irrigated farmland, industrial presence, and mobile home park density had clear connections to the composite scores. Sections with extensive irrigation, like Section 3, received lower Water Quality grades, highlighting the influence of agricultural runoff on nitrates. Areas with low industrial activity and few mobile home parks, such as Section 1, maintained higher scores, showing that multiple dimensions of human land use affect river health. By explicitly incorporating these land use metrics, the analysis moves beyond simply observing water quality trends to demonstrating how patterns of agriculture, development, and industrial activity interact to influence both ecosystem condition and overall watershed health.

Overall, the composite scores show how patterns of human land use and watershed management interact to shape river health. Sections downstream of intensive agriculture or with fragmented riparian habitat, particularly Section 3, consistently scored lower, while areas with balanced land use and healthier ecosystems, like Section 1, scored higher. These results highlight the importance of integrating land use, water quality, and ecosystem assessments to understand the full picture of watershed condition and guide management decisions along the Tuolumne River.