Presented by:

Modeling pesticide fate and 

transport through flowing water 

bodies for endangered species 

assessment in the California 

Central Valley

Lauren Padilla, Stone Environmental Inc.

Michael Winchell, Stone Environmental Inc.

Natalia Peranginangin, Syngenta Crop Protection, LLC

JiSu Bang, Syngenta Crop Protection, LLC

Katie Budreski, Stone Environmental Inc.

March 24, 2014
Introduction

 SWAT model application to 

agriculturally intensive Central 

Valley region in California for 

endangered species assessment

 Area of interest is CA Bay-Delta

− Estuary habitat

− Flowing water bodies are important 

species habitat

− Source of drinking water for many 

Californians

Critical Habitat Area

2
Overview

 Goal to estimate herbicide 

concentrations in Delta flowing 

water bodies

 Requires simulation of transport of 

pesticide residues from application 

sites upstream

 Model must address several key 

components 

− Hydrology

− Spray drift modeling

− Spatial and temporal distribution of 

applications

 Presentation of modeling 

approach to these components, 

then comparison of modeled and 

observed concentrations

Critical Habitat Area

3
Hydrology – Watershed Delineation

 A large, diverse watershed drains 

through Delta

 Included only model area below 

mountain reservoirs, upstream of use 

sites

− 24 freshwater reservoir outflows

− Drain 26,300 square miles or 40% of 

watershed area

− 30 year daily time-series of USGS inflows

− Some missing data linearly interpolated 

 Excluded Tulare and Kings River basins

− Only hydrologically connected during flood 

times

− Assume flood flows originate upstream of 

pesticide use

− Model flood flows as water inputs without 

pesticide residues using USGS data

Critical Habitat

4
Hydrology – Landscape Characterization

 Watershed area assessed:

− 344 subbasins with average area 

140km2 ranging from 0.01-1000 km2

− 37,041 Hydrologic Response Units 

(HRUs)

 This delineation was accomplished 

using high-resolution input data 

sets:

− Topography: 30-m NHDPlus V2 

Hydrologically Conditioned DEM 

(2012) (complies with HUC12 

boundaries)

− Soils Data: Soil Survey Geographic 

database, 1:24,000 scale (2012)

− Land Use Data: Cropland Data Layer 

(CDL), 30-m, multiple crop classes, 

classified into crop groups, dominant 

crop group taken based on 5-year 

composite (2007-2011)

Land use

Soils

DEM

HRUs

5
Hydrology – Weather Data

 Need to capture heterogeneity of 

climate across large modeled 

watershed area

 Historic temperature and 

precipitation data from nearest 

weather station supplied to each 

subbasin

− 30 years of daily data between 1981-

2010

− Data sources: Global Historical 

Climatology Network, Integrated 

Surface Database, California Irrigation 

Management Information System

− 51 temperature stations and 48 

precipitation stations with most 

complete records

− Missing data filled in by nearest 

secondary stations

Critical Habitat Area

6
Hydrology – Complex Flow Diversions

 Complex network of surface water 

control structures in and around Delta

− Time-varying flow

− High flow rates

− Lack temporal patterns

− Diverted to destinations hundreds of miles 

away

 Modified SWAT code to improve 

transport of water, chemical, and 

other dissolved and suspended masses

− Previously SWAT did not allow transport of 

water and mass according to historic timeseries 

− Our modification allows specification of 

daily- or monthly-average time-series

− Modification made possible modeling the 

many complex flow diversions

− Resulted in greatly improved accuracy of 

flows and chemical concentrations

 Examples:

− Flood control structures

− Irrigation canals

− Withdrawals by pumping plants

Tisdale Weir

CVP Jones Pumping Plant 7
Modeled Diversions – Daily time-step

 Modeled Weirs and Channels:

− Moulton, Colusa, Tisdale Weir transfers to 

Sutter Bypass

− Fremont, Sacramento Weirs to Yolo Bypass

− Delta Cross Channel connection to 

Mokelumne River

− Little Potato Slough connection to San 

Joaquin River

− All returned to watershed

 Modeled Pumping Plant Withdrawals:

− Central Valley Project Jones Pumping Plant 

to Delta-Mendota Canal

− State Water Project Banks Pumping Plant 

to CA Aqueduct

− Contra-Costa Canal

− All exported out of watershed

 Daily Datasets

− US Geological Survey, DAYFLOW

Sources: Exports and Flood Control, USGS and CA DWR

8
Modeled Diversions – Monthly time-step

 Modeled 33 irrigation diversions

 Can capture yearly variation with 

modified transfer scheme

 Monthly datasets 

− CA Department of Water Resources

One line per year

1981-2010

Sources: Full Watershed, USGS; 

Inlet locations, USGS; Diversion Locations, CA DWR

9
Modeled diversions – Improved Flow Rates

 Better magnitude and timing 

of flows

 Avoid compensating flow 

errors with calibration 

 More accurate prediction of 

pesticide concentrations

Observed Flow

Modeled Flow

Without transfers

With transfers

Subbasin 97, Sacramento below Wilkins

NSE: 0.91

RSR: 0.29

PBIAS: -2.44%

10
NSE: 0.94

RSR: 0.24

PBIAS: 17.37%

NSE: 0.99

RSR: 0.12

PBIAS: -10.0%

Modeled diversions – Improved Flow Rates

Observed Flow

Modeled Flow

Subbasin 219, San Joaquin near Vernalis Subbasin 183+190, Total Delta Outflow

Calibration period

Validation period

11
Pesticide Application Modeling - Spatial 

Distribution

 Annual application mass targets 

for each subbasin

− CA Pesticide Use Reporting (PUR) 

Database

− Highest use year between 2006-2010

− Max application rate with minimum 

interval according to label for each 

applicable land use

 Targets met by randomly choosing 

eligible HRUs within each subbasin

− Many different combinations of HRUs 

could meet annual subbasin target

− 100% of selected HRU area gets 

application at label rate

− If this would exceed the target, 

dynamically decrease applied area 

fraction of HRU to meet target

Critical Habitat

12
Pesticide Application Modeling – Temporal 

Distribution

 Probability distributions of 

applications occurring in each 

month for every subbasin and 

applicable land use

− PUR data between 2006-2010

− Application month drawn according 

to distribution

− Application day drawn with uniform 

probability

 For crops with applications made 

close to planting date, shift 

planting date after application 

date determined

 Ground and aerial application 

methods selected according to PUR 

probability

13
Spray Drift Modeling

 Potential water body areas

− 1:24,000 scale high-resolution NHD 

area features (USGS, 2012)

− Bay Inlet, Canal/Ditch, Foreshore, 

Sea/Ocean, Stream/River

 Ground spray drift fractions from 

AgDrift

− 50 in boom height

− Fine to medium/coarse droplet size

 Aerial spray drift fractions from 

AgDisp

− 10-20ft boom height

− 10mph windspeed

− Fine/medium droplet size Critical Habitat Area

14
Spray Drift Modeling

 Conducted proximity analysis of 

water body area within 400 m of 

each HRU

 Average drift fraction as a function 

of distance from HRU edge in 

ranges: 0-20 m, 20-40m, 40-60 m, 

60-120 m, 120-200m, 200-400m

 Drift mass input directly into 

flowing water bodies according to,

Critical Habitat Area Sources: Full Watershed, USGS; Water bodies, (1:24,000) CA NHD area; 

Critical Habitat, USFWS

15
Monte Carlo Simulations

 64 simulations sampling range of application timing and locations

− Accounts for variation in management practices among growers

− Application scenarios remain constant for each simulation year

 30-year simulations sampling range of weather conditions

 Substantial computational requirements

− Over 3 hours per run

− Developed software to automatically generate application scenarios and distribute runs 

among several processors

16
Simulated vs. Observed Concentrations

 Observed maximum 

concentrations were 

compared with modeled 90th

percentile concentrations.

 Modeled concentrations 

were same order of 

magnitude as monitoring 

data.

 Modeled EECs for variety of 

water body types: major 

rivers to small sloughs

 Data sources: CEDEN, 

NAWQA, NWIS, EPA STORET, 

CILRP Critical Habitat Area

17
Simulated vs. Observed Concentrations

 Comparison for the four reaches with the most detections

− San Joaquin near Vernalis (219), Patterson (235)

− Sacramento near Freeport (148)

− Tuolumne near Shiloh (227)

 77%-98% of observations below level of quantification. Minimum 

quantification (min LOQ): 0.001 ug/L 

Reach 148 Reach 219 Reach 227 Reach 235

Observed Max Conc. (ppb) 0.011 0.015 0.006 0.015

Modeled Max Conc. (ppb) 0.216 0.574 0.725 0.664

Modeled 99th %-ile Conc. (ppb) 0.020 0.008 0.006 0.014

Modeled 95th %-ile Conc. (ppb) 0.003 0.002 0.001 0.003

Observation days below LOC (%) 98 92 84 77

Modeled days below LOC (%) 91 92 96 91

18
Summary

 Comprehensive SWAT model for the CA Bay-Delta watershed capturing 

upstream pesticide use area

 Hydrology accounting for freshwater reservoir outflows, diversion of 

surface water and associated residues due to flood control, irrigation, and 

pumping

 Use of best available land use, soils, topography, weather, and pesticide 

use data

 Characterized pesticide applications according to ‘worst case’ historic use

 Realistic drift modeling based on actual water bodies

 Model concentrations compared well to monitoring data

19