For the nine months ended June 30, 2020, noninterest income was $8.0 million compared with $6.1 million for the nine months ended June 30, 2019. Loan swap fees were $1.2 million for the nine months ended June 30, 2020, compared to no similar fees in the comparable period in 2019. Gains on the sale of loans and investments and fee income from trust and investments also contributed to increased noninterest income.
Noninterest expense was $9.1 million for the three months ended June 30, 2020 compared with $9.5 million for the comparable period a year earlier. Noninterest expense was $28.7 million for the nine months ended June 30, 2020 compared with $28.9 million for the comparable period a year earlier.
Balance Sheet, Asset Quality and Capital Adequacy Review
Total assets increased $209.7 million to $2.01 billion at June 30, 2020, from $1.80 billion at September 30, 2019, primarily due to increases in cash and cash equivalents and loans receivable, offset in part by a decline in investment securities available for sale.
Cash and cash equivalents increased $118.6 million during the first nine months of fiscal 2020 as a result of the previously discussed pandemic-oriented balance sheet adjustments made to grow cash to mitigate potential liquidity risks. At June 30, 2020 cash and cash equivalents were $170.8 million compared with $52.2 million at September 30, 2019. The Company built the majority of its cash position in the fiscal second quarter of 2020 through increased borrowings and has maintained that position.
Total net loans increased to $1.42 billion at June 30, 2020 from $1.33 billion at September 30, 2019, reflecting growth in residential mortgages, construction loans and both commercial real estate and commercial and industrial loans. Residential real estate loans were $605.3 million at June 30, 2020, up $7.8 million from September 30, 2019. The Company sold $19.1 million in residential mortgage loans to the Federal Home Loan Bank of Pittsburgh during the fiscal year. Indirect auto loans declined $33.1 million to $48.9 million at June 30, 2020 from $82.0 million at September 30, 2019, reflecting expected runoff of the portfolio following the Company’s previously announced discontinuation of indirect auto lending in July 2018.
Commercial real estate loans were $508.1 million at June 30, 2020, up from $480.6 million at September 30, 2019. Commercial loans (primarily commercial and industrial) increased to $142.56 million at June 30, 2020 from $55.6 million at September 30, 2019 due primarily to PPP loans of $75.6 million.
Total deposits were $1.48 billion at June 30, 2020 compared with $1.34 billion at September 30, 2019 and were up 11.5% from $1.33 billion at June 30, 2019. Core deposits (demand accounts, savings and money market) were $984.7 million, or 66.3% of total deposits, at June 30, 2020 compared to $837.1 million, or 62.9% of total deposits, at June 30, 2019. Noninterest bearing demand accounts exhibited strong year-over-year growth, increasing 33.7% to $235.8 million, interest bearing demand accounts grew 30.8% to $238.4 million and money market accounts grew 2.8% to $351.5 million. Total borrowings increased $41.3 million to $289.5 million at June 30, 2020 from $248.3 million at September 30, 2019 as the Company borrowed additional funds from the FHLB Pittsburgh to increase cash reserves.
Nonperforming assets totaled $20.5 million, or 1.02% of total assets, at June 30, 2020, up from $10.3 million, or 0.57% of total assets, at September 30, 2019 and $19.1 million or 1.06% of total assets, at June 30, 2019. The allowance for loan losses was $14.3 million, or 1.00% of loans outstanding, at June 30, 2020, $12.6 million, or 0.94% of loans outstanding at September 30, 2019 and $12.6 million, or 0.94% of loans outstanding at June 30, 2019, primarily reflecting prudent reserving to match commercial loan growth, overall loan credit quality and decreasing charge-off trends. The primary reason for the increase in nonperforming assets at June 30, 2020 as compared to September 30, 2019 was the addition of two nonperforming commercial real estate loans totaling $9.3 million. These loans are well collateralized and carry personal guarantees.