Long-term environmental monitoring provides the broad spatial and temporal scale information important to developing realistic conceptual models of natural systems, and it represents the cornerstone approach to identifying when, where, and how humans impact those systems. With coastal populations growing worldwide, local monitoring programs will become increasingly critical to making sound management decisions. The South Carolina Estuarine and Coastal Assessment Program (SCECAP) has developed independent indices of water quality, sediment quality, biological condition measures, and overall habitat quality, each of which encompasses multiple indicators, to assess the health of the state's coastal waters on a recurring basis. This multi-agency cooperative program has identified regions of elevated estuarine habitat degradation associated with heavily urbanized water bodies as well as moderately degraded habitat in areas previously considered relatively pristine. Temporal trends suggesting increasing sediment contamination and declining overall habitat condition have also been documented on a state-wide basis, but further monitoring will be necessary to confirm these changes. These data have contributed to documenting consistent correlations between upland development and degraded water and sediment quality at the scale of 14-digit HUC watersheds. SCECAP has also contributed to developing a tidal creek classification scheme against which hypotheses involving water and sediment quality, biological community structure, and urbanization impact may be tested.