Although numerous studies on various aspects of endocrine axes and the physiology of both juvenile and adult life stages of several teleosts exists, studies characterizing the basic functions and cross-talk of endocrine axes during early developmental stages (i.e. embryonic to early feeding fry), in particular, are limited. The goal of this study was to characterize morphological and molecular effects in rainbow trout alevins after waterborne exposures to 17β-estradiol (E2 0.0008 to 0.5 μg/L), triiodothyronine (T3; 0.52 to 65 μg/L), and various co-treatments for 21 to 23 days. Interestingly, there was no consistent evidence that E2 alone influenced growth, development or deformity rates, nor the co-treatments of 0.02 and 0.1 μg/L of E2 with up to 65 μg/L of T3. However, 13 and 65 μg/L T3 alone expedited development and caused a unique opercular deformity not previously reported. Gene expression changes were observed, but these were mainly at the highest concentrations tested. These data suggest low-level E2 does not negate abnormal growth and development caused by hyperthyroidism and examining more time points is likely required to demonstrate a stronger response profile for individual hormones and endocrine axes cross-talk.