Sediments in urban drainage systems (UDS) significantly impact their operation, so effective strategies are required to reduce their negative effects. Monitoring sediment accumulation provides valuable insights into sediment characteristics, sediment transport dynamics, and system performance. However, the effectiveness of monitoring systems is limited due to cost constraints and installation challenges. This study describes the development and application of a new system based on temperature dynamics to measure sediment depths in sewer systems. The methodology involves the analysis of temperature time series under dry weather flow conditions to identify harmonic patterns between wastewater and sediment-bed temperatures. These patterns are increasingly attenuated by increasing sediment depth. This study combines a system called MONitoring Temperatures in SEdiments (MONTSE), which integrates a dual-probe heat-pulse (DPHP) method to characterize sediment thermal properties, and a surrogate model, which includes temperature pattern analysis, to estimate sediment depths. Likewise, laboratory-scale experiments were performed to validate the temperature monitoring system and the surrogate model performance. The maximum absolute errors in measured sediment depths were less than 22 mm, and the uncertainty of the system was estimated at ±7.3 mm. Groundbreaking measurements of thermal properties of UDS sediments were also reported. Reliable information on sediment depths and properties was provided, so the system could significantly optimize sewer system operation and cleaning strategies.