The usage of English prepositions by non-native speakers is notoriously problematic. The debate about whether prepositions should be memorised as distinct cases or introduced in the teaching process by demonstrating their multiple meanings as a network of related senses is more likely to be resolved by adhering to the latter, sometimes referred to as the motivated polysemy approach. We claim that semantic (non-)congruence between prepositional senses in L2 and in L1 is no less important. The present paper focuses on two English prepositions, in and on, as they are used by Lithuanian learners of English representing different language proficiency levels ranging from B1 to C2 (Council of Europe 2001). Adhering to the approach of motivated polysemy and, more importantly, to the principle of semantic congruence between the senses of the above English prepositions and their prototypical Lithuanian equivalents, we have established that in, which demonstrates a high degree of semantic congruence with its prototypical equivalent in Lithuanian, the locative case, seems to be less problematic to Lithuanian learners of English than on, which lacks semantic congruence with Lithuanian. The results of the study suggest that the teaching of prepositions should take into account (non-)congruence of prepositional meanings between the learners’ mother tongue and their L2.