Questions & Answers about Вода в реке была прозрачной.
Why is прозрачной in the Instrumental case instead of the Nominative прозрачная?
When an adjective describes the subject using the past tense of быть (here, была), it usually takes the Instrumental case. The Nominative (прозрачная) is occasionally used to emphasize a permanent, timeless characteristic, but the Instrumental (прозрачной) is the standard, natural choice in the past tense to describe the state of things at that specific moment in time.
Could I translate "clear water" using чистая instead of прозрачная?
It depends on what you mean by "clear." Прозрачная specifically means "transparent"—you can see through it. Чистая means "clean" (free of dirt, bacteria, or pollution). If a river is milky but unpolluted, it is чистая but not прозрачная. Here, the speaker is specifically noting the water's visual transparency.
Why is в реке placed immediately after вода rather than at the end of the sentence?
Placing в реке (in the river) right after вода (water) logically groups them together to mean "the river water." If you put it at the end (Вода была прозрачной в реке), the focus shifts slightly to the location, sounding more like "The water was transparent in the river (as opposed to somewhere else)."