Morphonotactics determines phonological conditions on sound sequences produced by morphological operations both with morphemes and across boundaries. This paper examines the historical emergence and the development of morphonotactic consonant clusters in Germanic, Slavic, Baltic, Romance and other languages. It examines the role of the following morphological preference parameters: (i) morphotactic transparency/opacity, (ii) morphosemantic transparency/opacity, (iii) morphological richness. We identify several diachronic processes involved in cluster emergence, production and change: vowel loss, Indo-European ablaut (and comparable Arabic processes), affixation, compounding, metathesis, final and consonant epenthesis. Additionally, we discuss predictions derived from the Net Auditory Distance principle, psycholinguistic evidence and language acquisition. We show that the majority of morphonotactic clusters arise, phonologically, from vowel loss, and morphologically from concatenation.