I had two pelvic ultrasounds done and they show that i have a complex 3.1cm cyst with a thin septation on my left ovary along with a separate cyst which is 2.3cm. on the right ovary, there is a 1.8 cm dominant cyst. can you explain this a little more?

Ask your GYN MD: Without seeing the pelvic ultrasound, it is difficult to "explain this a little more". Your GYN MD who ordered the ultrasounds should be the person doing the explaining.

Ovarian cysts: What defines a "complex ovarian cyst" is internal structure and increased blood flow detected by the "color-Doppler" application of the ultrasound done. The absence of increased blood flow, and structure in the cyst, with only a septum makes the probability of malignancy low. Check with your gyn physician, who may want to do a laparoscopic biopsy.