The Atlantic Ocean coastal zone of Maryland is important both ecologically and economically. Due to water quality issues, the coastal lagoons of Maryland have received considerable research attention, but little corresponding research in the coastal waters that exchange with the coastal lagoons. To better understand the linkages between the coastal ocean and the potential impacts of human activity on Maryland’s coastal zone, 5 research cruises (2018-2019) were completed to investigate concentrations of nutrients and emergent harmful algal bloom (HAB) species of concern (Dinophysis, Karenia, Pseudo-nitzschia). Nutrient and HAB species had high intra-annual variability, as well as geographic variability with relation to the inlets, coastal lagoons, and offshore discharge sites. The most significant determinants across all sampling locations, depths, and times were nitrate and ammonium. Continued eutrophication and climate change, as well as the impact of connected waterways, presents challenges for managing regional water quality issues in the coastal ocean.