Razorback suckers (Xyrauchen texanus) and Colorado pikeminnow (Ptychocheilus lucius) are two endangered species of cyprinids located in the San Juan River Basin. Numerous factors may be contributing to the decline of these fish populations including hydraulic alterations (impoundment; altered thermal and hydrological regimes), non-native species interactions and contaminants. An assessment of the physical (temperature, substrate, ultraviolet [UV] radiation), biological (macroinvertebrates), and chemical factors (metals, polycyclic hydrocarbons, other water quality factors) was conducted to determine whether these factors could be limiting populations at six sites within the San Juan River and at one site in Los PiÑos River. Metal concentrations in sediment, surface and pore-waters were low, although significant differences in surface waters were found between sites. Hazard Quotients were calculated and indicate the potential risk for adverse effects should be considered for aluminum, lead and copper. Toxic Unit modeling also suggested a potential toxicity from sediments at several sites. Concentrations of 16 Priority Pollutant polycyclic aromatic hydrocarbons (PAHs) were low in sediment, pore water and Semipermeable Membrane Devices. Several compounds were found that are known to be toxic to aquatic organisms following photoactiviation by UV-B radiation. However no significant mortality to juvenile Colorado pikeminnow occurred during in-situ exposures conducted in the presence and absence of UV radiation. Seven-d reproduction tests with Ceriodaphnia dubia revealed that sediment pore water reduced reproduction at several sites. Physical and chemical habitat factors potentially affecting the distribution and composition of the macroinvertebrate community were evaluated. Macroinvertebrate populations were significantly different across sites. Differences, however, were not related to metal or organic contamination. Physical habitat variables of temperature, current velocity, and substrate size were useful predictors of macroinvertebrate densities between sites. A comparison of invertebrate communities on natural and artificial substrates indicated that a lack of suitable substrate is the main factor limiting macroinvertebrate distribution and composition at our study sites. The artificial substrates collected a more diverse community, and contained from 5 to 538 times more taxa than the Hess samplers. Community metrics were statistically significant (P < 0.05) between artificial substrate and Hess sampling methods in unstable (sand, silt, embedded cobble) substrates. Statistical differences were not observed when substrates associated with healthy invertebrate communities (gravel, loose cobble) were encountered. Numerous factors may be impacting endangered fish populations of the San Juan River. However, the influence of contaminants has not been unequivocally demonstrated. Additional analysis of toxicity data, contaminants, an
