Physico-chemical parameters and bio-contamination assessment through protozoan cysts and helminths eggs were carried out from the period of June to September 2010 in order to appreciate the pollution of the Danube River Basin in Romania. It recorded a higher tenor in Magnesium ion (60 mg/L) with respect to the calcium ion (20 mg/L). Other ions identified at substantial proportions were iron (1.459 mg/L), manganese (6.583 mg/L), phenol (12.780 mg/L) and Aluminium (0.0441 mg/L). Twenty one ciliated protozoa were identified in our analysis of water in the Danube River. Prominent was the presence of Caenomorpha medusula and Metopus ovatus which are indicators of polysaprobity. Resistant forms of enteropathogenic protozoa were present in our samples. These are Cryptosporidium sp (65 oocysts/l in August), Entamoeba histolytica (22 cysts/L in September), Giardia sp with 30 cysts/L in August. The helminths identified were Ascaris lumbricoides, Clornochis sinensis, Diphyllobothium latum, Enterobius vermicularis, Heterophrys heterophrys, larva of strongiloides stercoralis and Taenia sp. There is a low impact of natural depollution mechanisms which can functionally reduce the impending effect of the communicable diseases that are being transmitted by humans who constantly explore this aquatic medium during their leisure or economic activities.