She was waving goodbye with eyes brimming with tears.

Literal

She [topic-は] eyes [at-に] tears [object-を] full floating, goodbye [quotative-と] hand [object-を] was-waving.

さよならと手を振っていた — the quotative と connects the farewell word to the waving gesture. ~ていた marks the ongoing action. A poignant farewell scene.