The sediment load from the drainage basin may play a key role in sustaining the fragile tidal and subtidal habitats of the Venice Lagoon, which underwent significant erosional losses in recent decades. Freshwater discharge and suspended sediment transport were studied in two estuarine sections of the main tributary of the lagoon, Dese River, employing acoustic instruments and analyzing sediment accumulation in the estuary through bathymetric measurements. The results for 2021 are discussed in terms of discharge, rainfall–runoff relationships, suspended sediment load, and the impact of floods. Compared to previous estimates from 1999, the mean water flow was similar in both years, but the annual suspended sediment load nearly doubled. A single flood event is described, which produced extreme sediment transport and delivered 21.8% of the annual load over a 22 h period. This study provides a framework for assessing whether the sediment load from the Dese River may offset degradation in the morphodiversity of its estuary and the habitats it supports. High-resolution monitoring of sediment delivery from the freshwater tributaries is emphasized as a critical approach for protecting the estuarine areas at the water–land interface of the Venice Lagoon.