The steel pipe piles in the deep-water trestle are flexible yet highly sensitive to faults. Currently, there lacks a simplified calculation method that comprehensively account for the pile’s deflection at the top, with considering the combined effects of geometric initial defects, construction loads, and water flow load. This deficiency makes it challenging to address the non-linear behavior of steel pipe piles in deep water, thus posing safety risks. To address this issue, the water flow load was simplified to an inverted triangle distribution load, and elastic stable equilibrium differential equations for the steel pipe pile, both below and above the water surface, were respectively adopted to derive a theoretical calculation formula for pile deflection with considering geometric nonlinearity. Building upon this foundation, steel pipe piles of varying lengths were selected as the research object to explore the influence of geometric initial defects and nonlinearity on pile deflection. Through theoretical deviation, the theoretical formula was further simplified for derivation, making it more practical for engineering applications. The analysis results show that with considering geometric nonlinearity, the simplified model yields significantly different load flow calculations compared with models that neglect geometric nonlinearity. This is more in line with the flexible structure’s response to water loads. Consequently, our study provides valuable support and practical technology for managing water load impacts and lateral control of steel pipe piles in steel trestle structures during their operational life.