Non-perennial rivers (NPRs) have three hydrological states; each state has its importance, function and implication for water resource management. The dynamics of these states have been inadequately assessed and understood. Hence, this study sought to determine the spatiotemporal variations in the hydrological conditions of NPRs, focusing on the Touws River–Karoo drylands and Molototsi River within the semi-arid region of the Limpopo Province of South Africa. Additionally, the study aimed to delineate and characterize the primary areas contributing to runoff in these two river systems. Sentinel-1 and Sentinel-2 satellite data sources were employed in this study. Specifically, the modified normalized difference water index (MNDWI) derived from Sentinel-2 was utilized to delineate water surface areas along the two rivers. Subsequently, these derived datasets were utilized to assess the hydrological states over a 32-month period (2019–2022). Based on the presence of water, the river's state was classified as flowing, pooled, or dry. The results showed that remote sensing can be used to determine the hydrological state of the two river systems with ~90% overall accuracy. However, there is about a 30% chance that a flow event can be missed using Sentinel-2 due to clouds and temporal resolution. Some of these gaps can be filled using synthetic aperture radar (SAR) data (Sentinel-1), as demonstrated with the Molototsi River. In the Molototsi catchment, the upper catchment contributes the majority of flows. For the Touws River, the southwestern part of the catchment was determined as the major contributing area for the observed flows. This suggests that the chosen observation site might not be representative of upper catchment dynamics; therefore, a monitoring site in the upper catchment is required. This study provided hydrological information and an approach that can be used to monitor the hydrological states for better understanding and management of NPRs and catchments.