Between 1995 and 1998 we studied the effects of water level, moon phase, and site on the number of caimans observed in spotlight surveys in the Mamirauá Sustainable Development Reserve, Brazilian Amazonia. Multiple linear regression analyses including water level of the Amazon River and the moon phase explained 91 and 73% of the variance in number of Melanosuchus niger seen in spotlight surveys in Lago Mamirauá and Cano Mamirauá, respectively, and 60 and 76%, respectively, of the variance in the number of Caiman crocodilus seen. Water level had a statistically significant and negative effect on the number of M. niger and C. crocodilus seen. Moon phase had no significant effect on the number of C. crocodilus seen, but more M. niger were detected in Lago Mamirauá on nights with more moon light. The regression equations derived for Lago Mamirauá and Cano Mamirauá did not adequately predict the variation in numbers seen in 18 other water bodies in the Mamirauá Reserve. Analysis of covariance showed an interaction between water level and site on the numbers of M. niger and C. crocodilus observed in the spotlight surveys in these water bodies, indicating that the effect of water level depends on the site. In these analyses, moon phase did not have a significant effect on either species, and there was no interaction between moon phase and site. To monitor natural tendencies, or impacts (e.g., controlled commercial hunting), on caiman populations of Mamirauá Reserve, it will be necessary to undertake regular spotlight surveys in many water bodies of all types at a narrow range of water level to have confidence in the results.