The aim of this study was to analyse the distribution characteristics of microplastics in lakes, assess their potential impacts on ecosystems, and explore effective management and control strategies. Despite a wealth of research focused on lake water, the variations in microplastics with offshore distance and their vertical distribution within the water column are not well understood. Here, we investigated the freshwater continuum from the inlet of Taihu Lake to the centre, and vertically from the surface to the bottom water. The results revealed that the distribution of microplastics (<5 mm in size) exhibited a clear spatial gradient. The microplastic abundance at the lake entrance was 2.12 times greater than that at the centre, and on the lake surface, the microplastic abundance was 1.36–1.69 times higher than that estimated from the water column. Notably, the proportion of small-sized microplastics (<0.1 mm) in the bottom water was 1.72 times higher than that in the surface water. The main types of polymers identified were polyamide (PA) and polyvinyl chloride (PVC), and their main sources may be from clothes washing and industrial activities. The Monte Carlo simulation results indicated that the overall risk of microplastics in surface water was higher than that in the water column, and the contributions of PVC and polyurethane (PU) to the ecological risk were 90.10% and 9.57%, respectively. Therefore, PVC and PU should be the priority of microplastic pollution control. This study provides the first comprehensive evaluation of the spatial ecological risk of microplastics in Taihu Lake, which improves our understanding of the distribution and environmental risks of microplastics in lake systems.