Water management in lowland areas usually aims to keep water tables within a narrow range to avoid flooding and drought conditions. A common water management target parameter is the depth of the canal water table below the surrounding soil surface. We demonstrated a method that rapidly determines canal water table depth (CWD) from airborne LiDAR data. The water table elevation was measured as the minimum value determined in a grid of 100 m × 100 m applied to a 1 m × 1 m digital terrain model (DTM), and the soil surface was calculated as the median value of values in each grid cell. Results for areas in eastern Sumatra and West Kalimantan, Indonesia, were validated against 145 field measurements at the time of LiDAR data collection. LiDAR-derived CWD was found to be accurate within 0.25 m and 0.5 m for 86% and 99% of field measurements, respectively, with an R2 value of 0.74. We demonstrated the method for CWD conditions in a drained peatland area in Central Kalimantan, where we found CWD in the dry season of 2011 to be generally below −1.5 and often below −2.5 m indicating severely overdrained conditions. We concluded that airborne LiDAR can provide an efficient and rapid mapping tool of CWD at the time of LiDAR data collection, which can be cost-effective especially where LiDAR data or derived DTMs are already available. The method can be applied to any LiDAR-based DTM that represents a flat landscape that has open water bodies.