The maritime environment is a very unique system with respect to the environmental conditions that affect the transmission of electromagnetic energy, and especially the part of the spectrum that falls in the infrared band. This paper proposes an end-to-end model for the detection of ships at the environmental conditions of the eastern Mediterranean Sea, with the use of a Forward Looking Infrared (FLIR) system. The model: a) covers the issues regarding the detection and classification of simple model targets in various states of temperature conditions, by applying the Moser and O'Neill criteria, b) takes into account existing environmental conditions, by using data obtained from the Hellenic National Meteorological Service (HNMS) and the British Atmospheric Data Centre (BADC) for the years 2004–05, and c) uses the LOWTRAN 7 code for the calculation of the transmission through the maritime atmosphere. In the calculation of the atmospheric transmission, turbulence is taken into account through the introduction of a Modulation Transfer Function (MTF), to model the specific phenomenon. The FLIR system is also modeled as a series of MTF functions, with each one of those covering the characteristics of major subsystems of the detection device. Finally, the observer's MTF is included in the model, and the probability of completing the specific task is calculated and presented for a range of observer to target distances.