Theory predicts that the strength and relative importance of forces  that structure communities will vary predictably with changes in environmental conditions and stress.  In this study, we used a comparative experimental approach to assess seasonal differences in bottom-up (nutrients) and top-down forces (herbivory) on changes in tropical eastern Pacific coral reef community structure during periods of increasing (January – March) and decreasing (April – June) upwelling intensity.  We found that as upwelling intensity increased, herbivores were unable moderate increases in total algal cover, which expanded into areas previously dominated by live coral.  However, as upwelling intensity declined, herbivores effectively reduced total algal cover and increased live coral cover.  Additionally, nutrient enrichment reduced coral cover both in the presence and absence of herbivores at the beginning of the upwelling season, which coincided with increased overall abundance of algal functional forms.  However, during the period of decreasing upwelling intensity, experimental nutrient enrichment effects were not significant.  Based on our findings, we conclude that both nutrients and herbivory are important factors in determining coral community structure, although the relative importance of each was influenced by seasonal changes in environmental conditions.  Large-scale changes in environmental conditions during upwelling, including increases in nutrients and decreases in temperature, decreased the relative importance of top-down forces in limiting algal cover as bottom-up forces appeared to become predominant.  Lastly, although top-down regulation did not limit increases in algal cover during upwelling, herbivores strongly enhanced coral community resilience to seasonal increases in algal overgrowth, reversing temporary shifts to greater algal dominance as upwelling subsided.