This article proposes effective power management and battery protection strategies for a solar photovoltaic (SPV) powered dual-battery supported standalone water pumping approach propelled by a permanent magnet brushless direct current (PMBLDC) motor. A drift-avoidance perturb and observe MPPT algorithm is employed in conjunction with a 3-stage interleaved boost converter (TSIBC) and proposes a switching control scheme to enable double-stage solar photovoltaic generation system (SPGS) to operate at its maximum accessible power point (MPP) irrespective of any variation in climatic condition. The proposed dual battery control scheme (DBCS), which integrates a primary battery with an auxiliary battery, is connected to the 310 V DC link. This dual battery setup utilizes a parallel-active configuration facilitated by two bidirectional DC-DC converters (BDCs). The core idea behind dualization aims to maintain the state of charge (SoC) of the primary battery within upper and lower limits with the help of an auxiliary battery unit and regulate the DC link voltage at 310 V during fluctuations generated in the protection period. This scheme significantly extends the battery's lifespan, achieving an estimated 800 to 1000 cycles by maintaining its depth of discharge (DoD) at a level of 70 %. A centralized power handling unit (CPHU) is integrated for both the BDCs to facilitate the operating mode selection and regulate DC link voltage by alternatively charging/discharging both batteries. This approach enhances overall system efficiency by eliminating the need to oversize the solar array by up to 46 %, which would have been necessary to fully charge both batteries simultaneously. Previously, the DC link voltage regulation relied solely on MPPT control, resulting in significant deviations (up to ±38.43 %) during battery overcharging/deep-discharging (SoC ≥ 90 %/SoC ≤ 20 %). This work proposes a solution using an auxiliary battery controller within the DBCS, achieving near-zero (±0.5 %) DC link voltage deviation under all operating conditions. The effectiveness of the suggested DBCS controller is validated through a time-domain simulation conducted in MATLAB/Simulink, alongside real-time hardware-in-the-loop (HIL) digital simulator using the OPAL-RT platform. The acquired results corroborate enhanced performance for the standalone water pumping system (WPS) and demonstrate a seamless shift from the normal operational mode to battery protection mode, while ensuring steady regulation of the DC link voltage.