Fine-scale habitat use and partitioning by fishes is difficult to observe in dynamic estuarine systems and, to date, habitat utilization information is primarily inferred from direct capture of organisms. In addition, the temporal domain of nekton movement and behavior remains largely undescribed as traditional observational techniques (i.e., optical methods) are impeded by physical characteristics of estuarine ecosystems (e.g., suspended load). We report on a recent effort to integrate high-resolution multibeam imaging sonars (ARIS and DIDSON) in intertidal and subtidal creek habitats to evaluate the behavioral patterns, abundance, and size of nekton moving between these two adjacent, interconnected habitats as a function of tidal forcing over 8 complete ebb-flood cycles. Fish abundance and movement were highly coordinated with water level patterns, suggesting that nekton were cued into moving between interconnected habitats at specific depths, and that movement was not always in the direction of water flow. This was observed during both day and night tidal cycles. Further, nekton utilized specific parcels of the water column rather than being ubiquitously distributed throughout the entire water column, suggesting that fish orient to discrete depth intervals despite the overall shallow depths (~2 m). By integrating advanced survey technologies, fine-scale temporal and spatial nekton habitat use and behavior patterns can be explored, potentially providing novel insights into the value of tidally-available salt marsh habitats at scales not previously described.