Based on the long-term ecological study in the Southern California Coastal Ecosystem (marine) and the Lake Biwa Ecosystem (freshwater), we aim to illustrate how human disturbance may affect the way that natural populations respond to climatic variation. For the marine ecosystem, we focus on fishing effects on exploited fish populations. Using greater than 50-year long larval fish time series collected from the southern California region, we consider fishing as a treatment effect in a long-term ecological experiment. Comparing the exploited versus unexploited species, we found that the long-term variability in the abundance of exploited species is higher than that of unexploited species, and geographic distributions of exploited species are more responsive to climate changes than those of unexploited species. These results suggest that fishing may reduce the resilience of fish populations facing environmental variation. For the freshwater ecosystem, we examine the eutrophication effects on zooplankton populations. Using greater than 40-year long plankton time series, we found that the enhanced total phosphorus and thus phytoplankton concentration from the late 60's to middle 80's resulted in high abundance of herbivorous zooplankton. The steady increase in water temperature of the lake along with invasive species may be detrimental to local zooplankton and fish populations.