In the area of the Neretva delta in the eastern Adriatic, where the European eel, Anguilla anguilla (Linnaeus, 1758) has been traditionally fished for centuries, a decline in its population has been observed, as in most of Europe. Despite several studies, systematic monitoring was not performed, and the causes of population decline are attributed to anthropogenic stressors, mainly overfishing and interventions that disrupt the migration. With the stock at a low level, there is a need for a detailed assessment of biological data and the determination of the “zero state” of the eel population in the areas where monitoring was not previously performed, such as the Neretva delta. This data would serve as a basis for the development of an appropriate monitoring and eel management plan. One of the under-researched aspects is still the eel’s morphology, which is closely related to all basic life functions. The aim of this work was to analyze in detail the morphological parameters of yellow and silver eels from the mouth of the Neretva River in different seasons and the relationships between the measured morphometric parameters and physiological indicators and to compare them with previously published results for different life stages across Europe. The samples were collected during spring, summer and autumn of 2021, and winter of 2022. Yellow eels were present in the catch throughout the sampling period, while silver eels were caught in the autumn and winter. Yellow and silver eels were significantly different regarding 22 morphometric measures that were analyzed. Isometric growth was recorded for yellow eels in the spring and autumn of 2021, and positive allometric growth was recorded for yellow eels in the summer and silver eels in the autumn of 2021 and winter of 2022. PCA showed that the main factor that separates the eels grouped by life stage in different seasons is the intestine length (IL), whereas the rest of the factors (weight—W; intestine weight—IW; liver weight—LW; and total length—TL) affect the groupings almost equally. Seasonal averages of the condition factor (CF) for yellow and silver eels did not differ statistically. Three indicators were used to describe intestine morphology: relative gut weight (RGW), relative gut length (RGL), and Zihler’s index (ZHI); and the only statistically significant difference between yellow and silver eels was recorded for the RGW. The hepatosomatic index (HSI) was significantly different between silver eels in winter and yellow eels in spring. In addition to supplementing the already known facts, this paper provides new information on the functional morphology of the European eel. Monitoring of these characteristics is crucial for management of the European eel fisheries as they are directly related to functional performance and affect the ability to maintain sustainable populations in anthropogenically altered environments.