To ensure a ship's fully operational status in a wide spectrum of missions, as passenger transportation, international trade, and military activities, numerous interdependent systems are essential. Despite the potential critical consequences of misunderstanding or ignoring those interdependencies, there are very few documented approaches to enable their identification, representation, analysis, and use. From the cybersecurity point of view, if an anomaly occurs on one of the interdependent systems, it could eventually impact the whole ship, jeopardizing its mission success. This paper presents a proposal to identify the main dependencies of layers within and between generic ship's functional blocks. An analysis of one of these layers, the platform systems, is developed to examine a naval cyber-physical system (CPS), the water management for passenger use, and its associated dependencies, from an intrinsic perspective. This analysis generates a three layers graph, on which dependencies are represented as oriented edges. Each abstraction level of the graph represents the physical, digital, and system variables of the examined CPS. The obtained result confirms the interest of graphs for dependencies representation and analysis. It is an operational depiction of the different systems interdependencies, on which can rely a cybersecurity evaluation, like anomaly detection and propagation assessment.