Check deposits are not reported as cash transactions regardless of the amount. The CTR filing requirement of $10k for cash transactions (including aggregate transactions over a short period of time -- that's what tripped up Eliot Spitzer) applies to the green (or pink or yellow these days) folding stuff, not to check payments.
On the other hand, transactions of ANY amount that depart from what is "normal" for your banking activities can be reported on a SAR or Suspicious Activity Report. And while you may be made aware of a CTR if one is filed, you generally will NOT be notified of a SAR if one is filed.
Most banks use sophisticated software to flag activity as "suspicious." Normally those are reviewed by a human before a SAR is generated. I used to work in the banking industry and we'd see SAR flags for things as innocuous as children making small cash deposits from a lemonade stand at 2 or 3 different branches. We didn't generate a SAR in those cases. On the other hand, the elderly gentleman who decided to supplement his retirement income by kiting checks (while wearing some VERY good disguises) and depositing the profits in his account DID trigger a SAR even though none of the amounts was more than a few hundred at one time. Prior to that point all of his deposits were ACH from Social Security and a monthly check from his son. The sudden infusion of a couple thousand in cash every month was suspicious and ultimately lead to his arrest.
BTW, while the reports are made to the Treasury Department, the IRS is the lead agency for Treasury on collection of CTR and SAR data. They routinely share this information with other law enforcement agencies AND use it for income verification at times.