In the context of smart agriculture, accurate soil moisture monitoring is crucial to optimise irrigation, improve water usage efficiency and increase crop yields. Although low-cost capacitive sensors are used to make monitoring affordable, these sensors face accuracy challenges that often result in inefficient irrigation practices. This paper presents a method for calibrating capacitive soil moisture sensors through data assimilation. The method was validated using data collected from a farm in Dos Hermanas, Seville, Spain, which utilises a drip irrigation system. The proposed solution integrates the Hydrus 1D model with particle filter (PF) and the Iterative Ensemble Smoother (IES) to continuously update and refine the model and sensor calibration parameters. The methodology includes the implementation of physical constraints, ensuring that the updated parameters remain within physically plausible ranges. Soil moisture was measured using low-cost SoilWatch 10 capacitive sensors and ThetaProbe ML3 high-precision sensors as a reference. Furthermore, a comparison was carried out between the PF and IES methods. The results demonstrate that the data assimilation approach markedly enhances the precision of sensor readings, aligning them closely with reference measurements and model simulations. The PF method demonstrated superior performance, achieving an 84.8% improvement in accuracy compared to the raw sensor readings. This substantial improvement was measured against high-precision reference sensors, confirming the effectiveness of the PF method in calibrating low-cost capacitive sensors. In contrast, the IES method showed a 68% improvement in accuracy, which, while still considerable, was outperformed by the PF. By effectively mitigating observation noise and sensor biases, this approach proves robust and practical for large-scale implementations in precision agriculture.