Shallow coastal bay-estuary systems have complex water quality dynamics due to wind effects and tidal currents. In these systems, hydroclimatic extremes (hurricanes, droughts etc.) and anthropogenic stresses (increasing agri- and aqua-cultural practices, upstream withdrawal of water, point sources of pollution etc.) have great impacts on water quality. Development of conservation and restoration strategies requires in-depth understanding of the spatiotemporal patterns of water quality parameters in these bay-estuary systems. Apalachicola Bay, in Northern Florida Gulf, is one of such systems, which has been experiencing water quality deterioration for decades. The objective of this study is to explore space-time structure of this system utilizing a long-term (2002-2023) dataset of physical-chemical water quality parameters (pH, water temperature, dissolved oxygen, salinity, specific conductivity, turbidity, dissolved inorganic phosphorus, dissolved inorganic nitrogen, and chlorophyll-a) monitored at nearly 20 stations in the bay. To analyze the spatiotemporal patterns in water quality, we apply statistical techniques such as monotonic/non-monotonic trend, changepoint detecting, clustering, discriminant, and complex network theory. Through these analyses, we aim to group the study bay-estuary system into homogenous geographic zones and seasons in terms of various water quality parameters. This study can assist in effective water quality management and contribute to scientific knowledge concerning spatiotemporal dynamics of water quality in estuarine-bay systems.