Microplastics (MPs) are widespread across environmental compartments and originate from land-based sources such as urban runoff, agriculture, wastewater treatment plants (WWTPs). Among these sources, WWTP bypass flows remain largely unknown, despite their relevance as contaminant inputs. Bypass flows may be activated during intense rainfall events, whose frequency is expected to increase due to climate change. During these events, untreated wastewaters are released into rivers discharging into receiving lake. Due to its semi-closed shape, long hydraulic residence time, and ecological importance, Lake Como represents a case study for evaluating how episodic untreated discharges and continuously treated effluent inputs influence contaminant dynamics in freshwater ecosystems. MPs were identified through fluorescence microscopy after Nile Red and Bengal Rose co-staining, while polymer composition and mass were determined by Pyrolysis–Gas Chromatography–Mass Spectrometry (Py–GC–MS). Results indicate that bypass flow events increase MP loads in the river flowing into the lake, contributing an estimated ~200 kg/year. Overall, lake showed low pelagic concentrations but pronounced accumulation in littoral zones and shallow sediments. Fine particles (<50 µm) and fragments dominated. Polyethylene (PE) and Polypropylene (PP) were the main polymers in waters, with Styrene Butadiene Rubber (SBR) prominent in stormwater, while sediments and hypolimnetic samples showed greater diversity (PE, PP, and Nylon 6,6). Results indicate that episodic bypass discharges may represent an underestimated pathway for MP inputs into freshwater ecosystems. Although pelagic concentrations remained generally low, MPs accumulated in littoral areas and shallow sediments, creating potential hotspots of exposure for benthic and nearshore organisms. The predominance of small particles (<50 µm) is of ecological concern, as these size fractions are more readily available for ingestion across multiple trophic levels. Under future climate scenarios, the increasing frequency of intense rainfall events may enhance untreated wastewater releases, potentially increasing MP exposure and ecological risks in freshwater food webs.