1

1 Part 3. Long-term Food Web and Ecosystem Monitoring 

2 Conceptual basis

3 As described in the preceding sections of this report, quantitative food webs developed for select 

4 reaches of the Colorado River provide strong evidence for both bottom-up and top-down control 

5 of the food web. This finding leads us to conclude there is not so much a need for monitoring of 

6 the “food base” as there is a need for monitoring key indicators of the food web and ecosystem 

7 as a whole. Put another way, we believe food web and ecosystem monitoring protocols should 

8 include traditional metrics of food availability for fishes (i.e., invertebrate drift measurements), 

9 but also ecosystem-process metrics that may not have a clear relation or link to food availability 

10 for fishes per se (i.e., DOC budgeting and production estimation). Such an integrated, ecosystem 

11 approach allowed us to easily reconcile counterintuitive food web responses to the 2008 artificial 

12 flood. Recall, a significant increase in rainbow trout populations occurred after the flood, in 

spite of a large decrease in total invertebrate production (~60% reduction, from 30 g AFDM m-213

yr-1to just 13 g AFDM m-2yr-114 ) that was largely driven by a 70% reduction in the production of 

a dominant taxon (G. lacustris; from ~8 g AFDM m-2yr

-1

to 2.5 g AFDM m-2yr

-1

15 ), which earlier 

16 investigators had concluded was a critical prey item for rainbow trout. This same 

17 counterintuitive ecosystem response would have confounded interpretation of traditional 

18 ‘foodbase monitoring’ indicators such as benthic invertebrate biomass. Although this food 

19 web/ecosystem approach represents somewhat of a departure from the current conceptual basis 

20 for Goal 1, we think this is a logical step in the overall process of “learning by doing” that is the 

21 hallmark of adaptive management. 

22 Designing a food web and ecosystem monitoring program for the Colorado River is complicated 

23 by the remote nature of the ecosystem, and complex spatial and temporal variation in key 

24 drivers. For example, the effects of Glen Canyon Dam and its operations (e.g., alterations in 

25 water temperature regimes, hydropeaking, etc.) are strongest in the tailwater, but the effects of 

26 turbidity moderate these effects further downstream. The degree of hydropeaking (i.e., daily 

27 range and average discharge) varies seasonally in response to changes in human demand for 

28 power, with the largest daily range and average volume occurring in winter and summer and 

29 lower daily range and average volumes occurring in spring and fall. Short-duration floods from 

30 tributaries (1-10 days) that deliver suspended sediment turbidity are strongly seasonal

31 (summer/fall monsoon season and winter snowmelt), and, importantly, the timing and duration 

32 of these floods is now independent and asynchronous with mainstem flow conditions. Water 

33 temperature regimes are also seasonal, but the timing of the annual minima and maxima that can 

34 serve as a cue for key invertebrate life-stage changes is relatively independent of local climate 

35 and therefore asynchronous with temperature regimes in tributaries that support source 

36 populations of native insect taxa (Olden and Naiman, 2009). In a system as complex as the 

37 Grand Canyon, there would appear to be countless ways to go about allocating limited resources 

38 and effort to food web and ecosystem monitoring. It is therefore essential that a food web and 

39 ecosystem monitoring program focus on the use of metrics that integrate across large spatial and 

40 temporal scales. The basis for this is further strengthened when one considers that Colorado 

41 River native fishes are highly mobile—fish populations are likely integrating food resources over 

42 similarly large spatial and temporal scales. 

43
2

44 Understanding the relative influence of natural environmental variation vs. Glen Canyon Dam 

45 operations on fish populations is of great importance to managers and a primary motivation for 

46 Goal 1 monitoring (see Table 3). Therefore, the process of determining appropriate spatial and 

47 temporal resolution for core monitoring should be informed by spatial and temporal trends in 

48 humpback chub and rainbow trout because these species motivate the vast majority of adaptive 

49 management experimentation. Indeed, two new management actions planned as part of the 

50 adaptive management process directly target these species (non-native rainbow trout control to 

51 benefit humpback chub), or will likely affect them (additional testing of artificial floods as a 

52 sediment conservation tool). Proposed non-native control includes direct removal of rainbow 

53 trout for large reaches of river, and rapid decreases in discharge designed to strand and kill 

54 juvenile rainbow trout in Glen Canyon. Our research findings suggest that these experimental 

55 actions will likely alter food web structure and ecosystem processes. A robust ecosystem 

56 monitoring program that integrates research and monitoring across Goals 1, 2, 4, 7 (i.e., 

57 foodbase, native fish, non-native fish, and water quality) will be critical to the process of 

58 identifying mechanisms underlying fish population response to these two planned management 

59 actions. 

60

61 Table 3. Goal 1 Core Monitoring Information Needs

1.1.1 Determine and track the composition and biomass of primary producers below Glen 

Canyon Dam in conjunction with measurements of flow, nutrients, water temperature, 

and light regime.

1.2.1 Determine and track the composition and biomass of benthic invertebrates below Glen 

Canyon Dam in conjunction with measurements of flow, nutrients, water temperature, 

and light regime. 

1.3.1 Determine and track the composition and biomass of drift in the Colorado River in 

conjunction with measurements of flow, nutrients, water temperature, and light regime.

62

63 Here, we outline what we believe are the critical elements to Goal 1 monitoring needed to meet 

64 the Core Monitoring Information Needs identified by the GCDAMP. This description is 

65 somewhat general in nature, omits detailed description of sampling per se, and emphasizes 

66 description of the overall approach; exact sample sizes, sampling locations, timing of sampling, 

67 etc. will be determined after consultation with permitting agencies (i.e., Glen Canyon NRA, 

68 Grand Canyon NP, US Fish and Wildlife Service), and after coordination and consultation with 

69 other GCMRC Programs (i.e., Goals 2, 4, and 7). Precise description of Goal 1 monitoring 

70 should only occur after consultation and coordination with monitoring programs for Goals 2, 4, 

71 and 7 to ensure it is completely integrated with these related efforts. 

72 Sampling Design and Approach

73 We propose monitoring the Colorado River food webs and ecosystem using many of the same 

74 approaches and techniques that were developed during the research phase of this project. We 

75 also propose evaluating some new metrics that integrate over large spatial and temporal scales,

76 and are therefore promising tools to be explored during implementation of long-term monitoring

77 in Grand Canyon. 

78

79 We suggest that frequent, near monthly, sampling of transported organic matter, primary 

80 production, invertebrate drift, and emergence production should occur at Lees Ferry, Phantom 
3

81 Ranch, Diamond Creek, the Little Colorado River itself, and in the Colorado River near the LCR 

82 confluence. The feasibility and utility of this intensive sampling approach was demonstrated at a 

83 subset of these sites during the research phase of the project. Although frequent sampling in the 

84 Little Colorado River and in the mainstem near the confluence presents a considerable challenge 

85 because of limited accessibility, long-term monitoring at these two locations is critical because of 

86 the strong effect this tributary has on Colorado River ecosystem processes, and because of its 

87 importance to humpback chub populations specifically. We propose frequent sampling in the 

88 Little Colorado River and near the confluence only during the first 1-2 years of monitoring 

89 implementation in order to identifying seasonal patterns in production and ecosystem processes. 

90 After 1-2 years of intensive effort at these sites, sampling effort may be reduced in an informed 

91 manner. For example, sampling could just target months that are most critical to young-of-year 

92 humpback chub. A monthly sampling regime in the Little Colorado River could reasonably be 

93 sustained for 1-2 years, even in the context of regular sampling at other several other sites, if 

94 LCR sampling trips were supported by helicopter. Long-term monitoring of the food web and 

95 ecosystem processes in the Little Colorado River will provide valuable information needed to 

96 evaluate the relative importance of this tributary versus the mainstem to humpback chub 

97 populations. Further, monitoring data from the Little Colorado River would help put similar data 

98 from the mainstem Colorado River into a larger context by allowing comparison to a system with 

99 a natural thermal and flow regime. 

100 

101 We additionally propose sampling benthic habitats throughout Glen and Grand Canyon once per 

102 year using river trips. Traditional benthic sampling represents an important, but relatively minor, 

103 component of the proposed monitoring strategy because these samples are integrating over small 

104 temporal and spatial scales, and collection of these samples in a large river with hydropeaking is 

105 extremely difficult. Frequent sampling at relatively few fixed sites will emphasize detection of 

106 temporal trends, particularly describing the effects of flow operations on the ecosystem, while 

107 less frequent river trip sampling across a large number of sites will emphasize detection of large108 scale spatial trends. To ensure the scope of inference for river trip sampling is truly canyon109 wide, we suggest sampling occur at the same location as intensive sampling, and also at 

110 additional random sites, similar to the approach for fish monitoring. 

111 Organic matter budgeting and primary production

112 Organic matter budgeting for long reaches of river provides a relatively quick and low-cost 

113 metric of ecosystem processes that nicely complements more robust continuous primary 

114 production measurements. We propose organic matter budgeting for four long reaches (Glen 

115 Canyon Dam to Lees Ferry, Lees Ferry to Little Colorado River confluence, LCR confluence to 

116 Phantom Ranch, Phantom Ranch to Diamond Creek; see Table 4) using monthly measurements

117 of all size fractions of transported organic matter and chlorophyll. Such a budgeting approach 

118 was conducted along two long reaches during the research phase of the project (Glen Canyon 

119 Dam to Lees Ferry, Lees Ferry to Grand Canyon). We propose segmenting the Grand Canyon 

120 reach with the addition of two sites to further resolve organic matter budgets for Marble Canyon 

121 versus the Colorado River below the LCR. Better resolving organic matter budgets and primary 

122 production in Marble Canyon will aid in understanding habitat quality for rainbow trout in 

123 Marble Canyon, and because autochthonous production from Marble Canyon is a potential 

124 subsidy to less productive reaches below the Little Colorado River. This approach to sampling 

125 will also allow us to determine whether Phantom Ranch, which is relatively accessible, is a 
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126 reasonable proxy for the Colorado River near the LCR confluence, which is relatively 

127 inaccessible. Exact methods and approaches will be developed in coordination with GCMRCs 

128 Lake Powell monitoring program, who will conduct sampling within Glen Canyon Dam, and 

129 also with the downstream water quality monitoring program, which conducts sampling and 

130 maintains equipment at the other proposed sampling locations. Sampling organic matter is 

131 relatively quick and low-cost. 

132 

133 As our research efforts identified, there is a critical need to begin resolving the relative 

134 importance of tributaries versus the mainstem to native fish production and population dynamics. 

135 We therefore suggest that long-term monitoring of primary production, transported organic 

136 matter, and chlorophyll from the Little Colorado River also be initiated. Regular, at least 

137 monthly collections, of organic matter and chlorophyll will be necessary to describe material 

138 budgets in the Little Colorado River in comparison to the mainstem river. Further, frequent 

139 servicing of water quality monitors will be required given the harsh conditions (i.e., heavy 

140 travertine deposition) in the LCR. Sampling in the Little Colorado River would be done in 

141 concert with sampling of the mainstem near the confluence. After 1-2 years of intensive 

142 sampling effort at both sites, we suggest the temporal frequency of sampling be reduced to 

143 critical seasonal time periods that are identified in collaboration with scientists studying 

144 humpback chub populations there. 

145

146 Table 4. Proposed long-term monitoring protocols for Goal 1 including sample type, frequency, 

147 and locations. 

Sample Type Sampling Frequency Locations

Ecosystem Metabolism Daily Lees Ferry, RKM48, RKM 100, RKM

140, RKM 266, RKM 362, Little 

Colorado River, Bright Angel Creek

Dissolved Organic Matter 10X per year Glen Canyon Dam, Lees Ferry, RKM 

100, RKM 140, RKM 362, Little 

Colorado River

Fine Particulate Organic Matter 

(<250 μm; to be processed for 

AFDM and chlorophyll a)

10X per year Glen Canyon Dam, Lees Ferry, RKM 

100, RKM 140, RKM 362, Little 

Colorado River

Coarse Particulate Organic 

Matter (>250 μm; to be 

processed for AFDM and 

chlorophyll a)

10X per year Glen Canyon Dam, Lees Ferry, RKM 

100, RKM 140, RKM 362

Invertebrate Drift 10X per year Lees Ferry, RKM 100, RKM 140, 

RKM 362, Little Colorado River, 

Bright Angel Creek

Emergent Insect Production 10X per year Lees Ferry, RKM 100, RKM 140, 

RKM 362, Little Colorado River

Benthic Algae and 

Invertebrates

1X per year Sites throughout Glen and Grand 

Canyon
5

148

149 We propose long-term chlorophyll monitoring and budgeting should employ multiple 

150 techniques. Fluorometry was used during the research phase of this project, while 

151 spectrophotometry has been used by GCMRCs Lake Powell monitoring program since its 

152 inception in 1990. Fluorometry is precise and low-cost; however, this technique may not always 

153 yield accurate results across the range of turbidity conditions typical of Grand Canyon. 

154 Spectrophotometry is more accurate, and less affected by sediment turbidity than fluorometry, 

155 but spectrophotometric determination of chlorophyll is far more expensive and difficult than 

156 fluorometers. Both techniques are considered acceptable methods for estimating chlorophyll by 

157 the US Geological Survey (USGS 2010). A long-term monitoring program for the Colorado 

158 River that employs both techniques will be the most robust. 

159

160 We also propose long-term monitoring of primary production at all organic matter budgeting 

161 sites (Lees Ferry, Little Colorado River confluence, Phantom Ranch, Diamond Creek, Little 

162 Colorado River) and two additional sites where ongoing water quality monitoring activities occur 

163 (RKM 48 and RKM 266). An expanded network of primary production monitoring will allow us 

164 to evaluate whether strong effects of flow operations on primary production observed at 

165 Diamond Creek are occurring throughout Grand Canyon. 

166 Invertebrate Drift and Emergence Production

167 We propose monitoring invertebrate response to changing flow and environmental conditions 

168 using invertebrate drift and emergence production measurements. Both types of samples can 

169 integrate over relatively large spatial and temporal scales, and therefore have the greatest 

170 potential to detect invertebrate response to major physical driers. Further, focal fish species—

171 rainbow trout and humpback chub—are both drift feeders, so invertebrate drift measurements 

172 will provide a direct metric of food availability to important fish species. 

173

174 The utility of invertebrate drift measurements was demonstrated during the research phase of this 

175 project at Lees Ferry; however, additional research and sampling is needed to identify the best 

176 technique for collecting invertebrate drift at proposed sites that are only hike-in accessible (see 

177 Table 4). To date, invertebrate drift sampling has been conducted using motorboats and in a 

178 depth-integrated fashion because this approach was recommended by the 2001 review panel

179 (Anders et al. 2001). Regular boat-based invertebrate drift sampling is possible at Lees Ferry 

180 and Diamond Creek, but this sampling technique is not possible at Phantom Ranch and the Little 

181 Colorado River confluence with the hike-in and helicopter supported approach being proposed. 

182 We suggest that paired collections of invertebrate drift samples using both boat- and shore-based 

183 techniques at Lees Ferry and Diamond Creek be conducted during the first year of monitoring to 

184 identify differences among methods. Only shore-based techniques will be used at other sites, 

185 except during annual river trips when both techniques can be used at these sites. This approach 

186 should provide the data needed to allow comparison of daily and annual invertebrate drift loads 

187 among sites. Even if the relation between boat and shore-based techniques is poor and difficult 

188 to describe statistically, data from each site will be internally consistent and useful for tracking 

189 trends at those sites through time. Invertebrate drift sampling in the Little Colorado River will 

190 follow protocols established for wadeable streams; drift nets equipped with flow meters will be 

191 anchored to the river bottom. 

192
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193 Collecting invertebrate drift samples that are integrated over longer time periods than 5 minutes 

194 is another area worth exploring as core monitoring is implemented. During the research phase of 

195 the project, we settled upon 5 minute tows because this was the maximum amount of time 

196 technicians could be expected to continuously raise and lower a 75 lb sounding weight. 

197 Integrating drift samples over longer time periods (i.e., hours) is commonly done in drift studies 

198 in small streams (Smock 2006). Long-duration drift samples could be collected from the center 

199 of the channel at Lees Ferry by attaching nets to existing navigation buoys; however, long200 duration drift sampling at other sites is only feasible if done near-shore. In essence, there 

201 appears to be a tradeoff among the two sampling approaches we recommend exploring—boat 

202 based techniques allow for better spatial integration while shore-based techniques allow for 

203 greater temporal integration of samples. Additional research is needed to further evaluate these 

204 apparent tradeoffs. 

205 

206 Although estimating emergence production has never been attempted in Grand Canyon, it 

207 appears to be a promising tool for long-term ecosystem monitoring. There is a strong 

208 relationship between benthic production and emergence production (Statzner and Resh, 1993; 

209 Gratton and VanderZanden, 2009), so estimating the flux of insects that are emerging from the 

210 Colorado River should provide an indicator of overall benthic insect production. Further, 

211 because the two insect taxa that dominate invertebrate production at downstream locations (i.e., 

212 Simuliidae and Chironomidae) also have high interaction strengths with fishes, monitoring 

213 emergence production may provide a metric of food availability that complements drift 

214 measurements. 

215

216 Measurement of emergence production has the added strength of integrating across the 

217 terrestrial-aquatic interface. Long-term monitoring of emergence could greatly increase our 

218 understanding of the potential importance of aquatic subsidies to adjacent terrestrial ecosystem. 

219 Ecological theory suggests (River Continuum Concept; Vannote et al. 1980), and our own 

220 empirical work on the Colorado River confirms (Kennedy and Ralston, 2012), that terrestrial-to221 aquatic subsidies are relatively minor in a system as large as the Colorado River, but emergence 

222 production could represent an important organic matter flux supporting terrestrial food webs in 

223 the Grand Canyon.

224

225 Samples of emergent insects are far easier and quicker to process than traditional benthic

226 samples because there is little organic matter or debris on emergence samples, and winged adults

227 are easier to identify than aquatic larvae. This is an important consideration in the selection of 

228 monitoring metrics because a program that emphasizes samples that are quick and easy to 

229 process is more likely to provide timely information to decision makers relative to a program that 

230 emphasizes samples that are difficult and time-intensive to process. 

231

232 We propose evaluating the utility of emergence production as monitoring metric by continuously 

233 deploying sticky traps at the three accessible locations, Lees Ferry, Phantom Ranch, and 

234 Diamond Creek (Table 4). Acetate sheets (8 1⁄2 x 11 in) will be covered with a thin coating of 

235 Tanglefoot ® and then deployed along multiple transects perpendicular to shore. Traps will be 

236 deployed using natural materials (i.e., sticks, rocks, vegetation) or small pieces of re-bar. Traps 

237 will be located away from established camps or day-use areas to minimize visitor impact. Sticky 

238 traps could also be deployed from existing USGS cableways at these three locations. Deploying 
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239 traps from cableways has several advantages including an identical spatial distribution of traps 

240 among locations, and sampling across the entire river surface, as opposed to transects that run 

241 parallel to shore. Both approaches to trap deployment could be tried during initial testing of this 

242 metric. 

243 Benthic algae and invertebrate biomass

244 Traditional benthic sampling of invertebrates is another important part of a food web and 

245 ecosystem monitoring strategy because it will provide information on the non-insect taxa that 

246 tend to dominate production budgets, but do not emerge or drift, and would therefore be missed 

247 using just drift and emergence measurements. However, directly sampling benthic habitats in 

248 the Colorado River is extremely difficult and time intensive, which limits the utility of benthic 

249 biomass as a monitoring metric. For example, hydropeaking constrains benthic sampling to a 

250 brief window of low water that varies in timing throughout the canyon (i.e., low water at the 

251 RKM 48 site typically occurred during the late morning while low water at our RKM 100 site 

252 occurred during the middle of the night), which greatly limits the area of habitat that can be 

253 sampled in a day. Further, just a small percentage of benthic habitats can actually be sampled 

254 (<20%) due to the constraints that depth and velocity create. Individual benthic samples are 

255 integrating over very small spatial scales, so they have limited value as an ecosystem monitoring 

256 index unless they are collected over large areas. Benthic samples can also take considerable time 

257 and effort to process because of abundant inorganic and organic debris. 

258

259 We therefore propose traditional benthic sampling should only occur once per year and that 

260 when this occurs, benthic habitats throughout Grand Canyon should be sampled using river trips. 

261 We recommend benthic sampling be done in association with lower monthly discharge volumes 

262 to facilitate integrating sampling effort over the largest area logistically possible. We propose 

263 sampling all habitat types, not just the most productive ones (i.e., cobble), in order to develop 

264 habitat-weighted estimates of algae and invertebrate abundance, biomass, and composition that 

265 can be compared among years. These data will provide a comprehensive snapshot of the benthic 

266 environment in Grand Canyon that can be repeated annually and will allow for detection of 

267 major trends such as the arrival of new invertebrate taxa, or changes in the diversity or richness 

268 of the invertebrate assemblage. A detailed benthic sampling design that incorporates randomly 

269 selected sites will be developed in consultation with GCMRCs research statistician to ensure the 

270 scope of inference for these samples is canyon-wide. 

271

272 Organic matter sampling will follow specific methods developed during the research phase of the 

273 project and that are described in detail in Rosi-Marshall et al. (2010). Individual rocks will be 

274 collected from cobble habitats, and all algae will be removed from rocks by scrubbing the rock 

275 with a wire brush in a small bucket of water. The volume of the resulting slurry will be 

276 estimated in a graduated cylinder. Small sub-samples of the slurry will be put onto glass fiber 

277 filters for determination of ash-free dry mass and chlorophyll concentration. The surface area of 

278 the rock will be estimated by taking a digital photograph of the rock on a piece of gridded paper 

279 and then using image analysis software to determine the area of the rock. Algae on cliff faces 

280 and irregular talus slopes will sampled using a modified syringe sampler. Depositional 

281 environments will be sampled using a Ponar dredge sampler. Estimates of ash-free dry mass and 

282 chlorophyll content on these habitats will follow the same sub-sampling procedures outlined 

283 above.
8

284

285 Invertebrate sampling will follow methods described in Cross et al. (2011). A Hess sampler will 

286 be used to sample cobble habitats in Glen Canyon, while individual rocks will be picked up from 

287 more downstream reaches because of armoring there. Rocks will be scrubbed in a large bucket 

288 to remove invertebrates. Samples will be preserved in the field using ethanol and then processed 

289 in the lab by size fraction. 

290

291 We propose long-term storage of the processed invertebrate samples should be done using 

292 formalin. This will result in a large collection of samples that need to be cataloged and 

293 maintained, increasing overall monitoring program costs. However, we feel archiving benthic 

294 invertebrate samples is warranted given the potential importance of the samples in answering 

295 novel questions that will only occur to scientists or managers post hoc; a hallmark of long-term 

296 monitoring is the ability to go back to archived samples and verify conclusions, or ask fresh 

297 questions. 
9

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