The study considers two phenomena in shallow water, which are thermal-driven circulation that is generated from heterogeneous horizontal temperature distributions, and sediment transport processes that occur around newly-built coastal structures. First, a theoretical understanding of thermal-driven flow within emergent vegetation is developed over diurnal cycles. During the daytime, across a sloping bottom, uniform incoming solar radiation creates warmer water in shallow regions and colder water in deep regions. The difference in horizontal temperature leads to pressure gradient and generates circulation from shallow to deep waters along the water surface and uphill near the sloping bottom. At night, the processes and the circulation patterns are reversed. In shallow water, abundant vegetation imposes inherent drag on the flow and can alter the heat distribution in the water body. Two models are included, one with a uniform distribution of solar radiation over the water column (unstratified), and one in which solar radiation decays exponentially with depth (stratified). A small bottom slope is assumed and asymptotic solutions are developed. For both models, viscosity is dominant in shallow water; while vegetative drags prevail in deep water. Distributions of vegetation can significantly alter the magnitude and patterns of circulation. Second, coastal processes are studied through the combined use of subbottom profiler (SBP) and ground-penetration radar (GPR) to measure bathymetry and sediment sublayers in shallow water. The advantage of this combined technique is a reduction of the limitations posed by the individual methods. In addition, utilizing signal responses from lake or river bottoms, an algorithm integrating SBP and GPR signals was established to estimate sediment porosity and the thickness of the top sediment layer. Through successive surveys, changes of bathymetry and sediment layer thickness were obtained and used to describe sediment erosion and deposition patterns. The integrated geophysical techniques were applied at a site near Concordia University on Lake Michigan to investigate changes in the nearshore environment and downcutting (vertical lowering) rates after the coastal structures are built. The results provide information on bathymetry changes, downcutting rates and longshore currents hindcast from the meteorological data, which can possibly explain recent bluff slumping in the south shores.